knitr document van Steensel lab
TF reporter barcode processing - pMT02 - K562
Introduction
18,000 TF reporters on pMT02 were transfected into mESCs, U2OS & A549, sequencing data yielded barcode counts of these experiments. These counts will be processed in this script.
Analysis
Based on these plots I will remove all samples that have less than 1,600 highly expressing barcodes, and all samples that have a correlation with the pDNA-bc counts of more than r=0.85
Normalization of barcode counts:
Divide cDNA barcode counts through pDNA barcode counts to get activity
Calculate mean activity - filter out outlier barcodes
Calculate correlations between technical replicates
Session Info
paste("Run time: ",format(Sys.time()-StartTime))## [1] "Run time: 25.89327 secs"getwd()## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/gen-1_K562"date()## [1] "Fri Mar 12 13:40:16 2021"sessionInfo()## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
##
## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] knitr_1.30 gridExtra_2.3 RColorBrewer_1.1-2
## [4] readr_1.3.1 haven_2.2.0 ggbeeswarm_0.6.0
## [7] plotly_4.9.2.1 tibble_3.0.1 dplyr_0.8.5
## [10] vwr_0.3.0 latticeExtra_0.6-29 lattice_0.20-38
## [13] stringdist_0.9.5.5 GGally_1.5.0 ggpubr_0.2.5
## [16] magrittr_1.5 ggplot2_3.3.0 stringr_1.4.0
## [19] plyr_1.8.6 data.table_1.12.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.5 tidyr_1.0.0 png_0.1-7 assertthat_0.2.1
## [5] digest_0.6.27 mime_0.9 R6_2.5.0 evaluate_0.14
## [9] httr_1.4.1 pillar_1.4.3 rlang_0.4.8 lazyeval_0.2.2
## [13] rmarkdown_2.5 labeling_0.3 htmlwidgets_1.5.2 munsell_0.5.0
## [17] shiny_1.4.0 compiler_3.6.3 vipor_0.4.5 httpuv_1.5.4
## [21] xfun_0.19 pkgconfig_2.0.3 htmltools_0.5.0 tidyselect_1.1.0
## [25] reshape_0.8.8 viridisLite_0.3.0 later_1.1.0.1 crayon_1.3.4
## [29] withr_2.1.2 grid_3.6.3 xtable_1.8-4 jsonlite_1.7.1
## [33] gtable_0.3.0 lifecycle_0.2.0 scales_1.1.0 stringi_1.5.3
## [37] farver_2.0.1 ggsignif_0.6.0 reshape2_1.4.4 promises_1.1.1
## [41] ellipsis_0.3.0 vctrs_0.2.4 tools_3.6.3 forcats_0.4.0
## [45] glue_1.4.2 beeswarm_0.2.3 purrr_0.3.3 hms_0.5.3
## [49] crosstalk_1.0.0 jpeg_0.1-8.1 prettydoc_0.4.0 fastmap_1.0.1
## [53] yaml_2.2.1 colorspace_1.4-1